dxpy 0.366.0__tar.gz → 0.367.0__tar.gz

{dxpy-0.366.0 → dxpy-0.367.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.366.0
+Version: 0.367.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.366.0 → dxpy-0.367.0}/dxpy/bindings/apollo/dataset.py

@@ -109,8 +109,9 @@ class Dataset(DXRecord):
 
     def assay_names_list(self, assay_type):
         assay_names_list = []
-        for assay in self.assays_info_dict[assay_type]:
-            assay_names_list.append(assay["name"])
+        if self.assays_info_dict.get(assay_type):
+            for assay in self.assays_info_dict.get(assay_type):
+                assay_names_list.append(assay["name"])
         return assay_names_list
 
     def is_assay_name_valid(self, assay_name, assay_type):

{dxpy-0.366.0 → dxpy-0.367.0}/dxpy/cli/dataset_utilities.py

@@ -1221,7 +1221,7 @@ def extract_assay_expression(args):
                 )
             )
     elif not args.assay_name:
-        if len(dataset.assays_info_dict["molecular_expression"]) == 0:
+        if dataset.assays_info_dict.get("molecular_expression") is None or len(dataset.assays_info_dict.get("molecular_expression")) == 0:
             err_exit("No molecular expression assays found in the dataset")
 
     # Load args.filter_json or args.filter_json_file into a dict
@@ -1391,7 +1391,7 @@ def extract_assay_expression(args):
     url = dataset.vizserver_url
 
     # Create VizClient object and get data from vizserver using generated payload
-    client = VizClient(url, project)
+    client = VizClient(url, project, err_exit)
     if args.sql:
         vizserver_response = client.get_raw_sql(vizserver_payload, record_id)
     else:

{dxpy-0.366.0 → dxpy-0.367.0}/dxpy/dx_extract_utils/filter_to_payload.py

@@ -228,6 +228,15 @@ def final_payload(
 
     order_by = [{"allele_id":"asc"}]
 
+    # In order for output to be deterministic, we need to do a secondary sort by sample_id
+    # if it is present in the fields
+    sample_id_present = False
+    for field in fields:
+        if "sample_id" in field:
+            sample_id_present = True
+    if sample_id_present:
+        order_by.append({"sample_id":"asc"})
+
     final_payload["order_by"] = order_by
     final_payload["fields"] = fields
     final_payload["adjust_geno_bins"] = False

dxpy-0.367.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.367.0'

{dxpy-0.366.0 → dxpy-0.367.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.366.0
+Version: 0.367.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.366.0 → dxpy-0.367.0}/test/test_extract_expression.py

@@ -1131,7 +1131,10 @@ class TestDXExtractExpression(unittest.TestCase):
         return process
 
     def test_dx_extract_cmd_location_expression_sample_sql(self):
-        expected_sql_query = ["SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` <= 8693350 AND `expr_annotation_1`.`end` >= 67440200) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` <= 148500700 AND `expr_annotation_1`.`end` >= 148994424) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` <= 75228160 AND `expr_annotation_1`.`end` >= 75235759)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2')", "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2')"]
+        expected_sql_query = [
+            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` <= 8693350 AND `expr_annotation_1`.`end` >= 67440200) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` <= 148500700 AND `expr_annotation_1`.`end` >= 148994424) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` <= 75228160 AND `expr_annotation_1`.`end` >= 75235759)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
+            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
+        ]
         response = self.run_dx_extract_assay_expression_cmd(
             self.expression_dataset,
             EXPRESSION_CLI_JSON_FILTERS["positive_test"]["location_expression_sample"],
@@ -1187,7 +1190,7 @@ class TestDXExtractExpression(unittest.TestCase):
         self.assertEqual(len(expected_X_chrom_response), 5)
 
     def test_dx_extract_cmd_sample_ids_with_additional_fields(self):
-        expected_sql_query = "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start`, `expr_annotation_1`.`end` AS `end`, `expr_annotation_1`.`strand` AS `strand` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE `expression_1`.`sample_id` IN ('sample_1')"
+        expected_sql_query = "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start`, `expr_annotation_1`.`end` AS `end`, `expr_annotation_1`.`strand` AS `strand` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE `expression_1`.`sample_id` IN ('sample_1') ORDER BY `feature_id` ASC, `sample_id` ASC"
         response = self.run_dx_extract_assay_expression_cmd(
             self.expression_dataset,
             EXPRESSION_CLI_JSON_FILTERS["positive_test"][

dxpy-0.366.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.366.0'